Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Segregation analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 829 records · Page 46Linked to original sources
PubMed1998

A high-resolution linkage map of the citrus tristeza virus resistance gene region in Poncirus trifoliata (L.) Raf.

Resistance to citrus tristeza virus (CTV) was evaluated in 554 progeny of 10 populations derived from Poncirus trifoliata. A dominant gene (Ctv) controlled CTV resistance in P. trifoliata. Twenty-one dominant PCR-based DNA markers were identified as linked to Ctv by bulked segregant analysis. Of the 11 closest markers to Ctv, only 2 segregated in all populations. Ten of these markers were cloned and sequenced, and codominant RFLP markers were developed. Seven RFLP markers were then evaluated in 10 populations. Marker orders were consistent in all linkage maps based on data of single populations or on combined data of populations with similar segregation patterns. In a consensus map, the six closest marker loci spanned 5.3 cM of the Ctv region. Z16 cosegregated with Ctv. C19 and AD08 flanked Ctv at distances of 0.5 and 0.8 cM, respectively. These 3 markers were present as single copies in the Poncirus genome, and could be used directly for bacterial artificial chromosome library screening to initiate a walk toward Ctv. BLAST searches of the GenBank database revealed high sequence similarities between 2 markers and known plant disease resistance genes, indicating that a resistance gene cluster exists in the Ctv region in P. trifoliata.

Chromosome Mapping↗
PubMed1995

Genetic epidemiology of breast cancer: interest of survival analysis methods.

In an attempt to explain the controversy resulting from the analysis of the breast cancer data collected by Jacobsen, a segregation analysis was performed using successively the unified mixed model (UM) and the logistic hazard function model (LHM) (Abel & Bonney, 1990). Under the UM, age of onset of the disease cannot be taken into account, each individual being assigned to a liability class according to his age at examination, whereas, in the LHM, variable age of onset is modelled using survival analysis methods. Under the UM, we confirmed the results of Demenais et al. (1986b), i.e. the transmission probabilities are significantly different from Mendelian expectations. The same results were obtained when taking into account the specific mortality for the computation of the morbid risk observed in a given liability class. Under the LHM, the analysis provides evidence for a monogenic autosomal model with a rare dominant allele responsible for the disease, and transmission probabilities compatible with Mendelian expectations. This study shows that the rejection of the Mendelian transmission under the UM can be due to a violation of a constraint of this model (i.e. the probability of being and not being affected in a given liability class should sum to 1) when a specific mortality is induced by the disease as in breast cancer. Survival analysis methods avoid these problems by taking into account the onset of the disease as the failure time event and are more suitable when studying a complex trait such as breast cancer.

Breast Neoplasms↗
PubMed2004

Familial central precocious puberty suggests autosomal dominant inheritance.

The prevalence of precocious puberty is higher in certain ethnic groups, and some cases may be familial. The aim of this study was to investigate the mode of inheritance of familial precocious puberty and to identify characteristics that distinguish familial from isolated precocious puberty. Of the 453 children referred to our center for suspected precocious puberty between January 1, 1997, and December 31, 2000, 156 (147 girls and 9 boys) were found to have idiopathic central precocious puberty, which was familial in 43 (42 girls and 1 boy) (27.5%). Data of the familial and sporadic cases were compared. The familial group was characterized by a significantly lower maternal age at menarche than the sporadic group (mean, 11.47 +/- 1.96 vs. 12.66 +/- 1.18 yr; P = 0.0001) and more advanced puberty at admission (Tanner stage 2, 56.5% vs. 78.1%; P = 0.006). Segregation analysis was used to study the mode of inheritance. The segregation ratio for precocious puberty was 0.38 (0.45 after exclusion of young siblings) assuming incomplete penetrance and 0.58 (0.65 after exclusion of young siblings) assuming complete ascertainment. These results suggest autosomal dominant transmission with incomplete, sex-dependent penetrance.

Adult↗
PubMed1999

[Burden of hereditary diseases in residents of the Mari El Republic].

A summary of the medical genetic studies of the Marii El population is presented. A total of 276,900 people, 110,894 and 166,006 urban and rural inhabitants, respectively, were examined. Regarding the ethnic composition, the studied population was mostly Mari (61.96%) and Russian (32.04%). Medical genetic examination revealed 480 subjects from 260 families with autosomal dominant (AD) diseases, 234 subjects from 184 families with autosomal recessive (AR) diseases, and 49 subjects from 41 families with x-linked diseases. Segregation analysis revealed a good agreement between the expected and observed segregation frequencies for families with AR and AD diseases and allowed the frequency of hereditary diseases in the urban and rural, as well as the Russian and Mari, populations, to be estimated. The total frequency of AD diseases in Maris was approximately twice as high as in Russians (1.99 and 0.97%, respectively); substantial differences between district populations were found. The total frequency of AR diseases was also two times higher in Maris than in Russians (1.00 and 0.54%, respectively). The frequencies of AR and AD diseases in different districts were correlated with the levels of random and local inbreeding, population size, and the index of maximum selection.

Genes, Dominant↗
PubMed1979

[Problems in the genetics of peptic ulcer. I. The nature of the inheritance and an analysis of different forms of the disease].

The analysis of literary data on the genetic investigation of duodenal ulcer is given. The investigation proper represents the analysis of 537 pedigree probands with various forms of duodenal ulcer and of 600 families of the control group. Basing on the analysis of distribution of frequency of forms of the disease, segregation analysis, as well as the distribution of forms of duodenal ulcer depending on the sex and age of the manifestation, the discrepancy is demonstrated of the opinion that duodenal ulcer is a monogenic disease, and a conclusion is drawn about the polygen conditionality of genetic component of various forms. The data have been obtained testifying in favour of a considerable heterogeneity of the duodenal ulcer and also the importance of the contribution to the genetic factors in the realization of different forms of the disease, which are approximately 60%. Some difficulties are illustrated, arising during the analysis of multifactorial disease, and the necessity is demonstrated of accounting its certain features (e.g. sex, the age of manifestation) during the interpretation of the results obtained.

Adolescent↗
PubMed1997

[Medico-genetic study of residents of Marii El republic: burden of hereditary diseases in four regions of the republic].

A medical genetic study of Orshanskii, Morkinskii, Sovetskii, and Semurskii raions (districts) of the Marii El Republic was performed. The total number of subjects examined was 115,743. Meadow Maris and Russians accounted for the most part of the populations of the districts studied. A total of 147 families with presumably autosomal dominant (AD) pathology and 150 families with presumably autosomal recessive (AR) or X-linked pathology (270 and 169 affected persons, respectively) were revealed. Segregation analysis demonstrated a good agreement between the observed and expected segregation frequencies for both AR and AD diseases, as well as a considerable number of sporadic cases of presumably AD diseases. The incidence of hereditary diseases was estimated separately for different population groups. Significant differences in this incidence were revealed between the urban and rural, as well as between the Russian and Mari populations; the average incidence was 2.33 affected subjects per 1000 people. The incidence of AR diseases was significantly higher in Maris than in Russians (1.34 x 10(-3) and 0.82 x 10(-3), respectively). The populations studied exhibited a significant, high correlation between the incidence of AR diseases and the levels of random and local inbreeding. The incidence of X-linked recessive diseases was approximately the same as in Russian populations studied earlier. Its average value was 0.5 per 1000 men; the incidence in the Mari and Russian populations did not differ significantly. The higher AD incidence in the total population studied and the higher AR incidence in the Meadow Mari population compared to the populations studied earlier are discussed.

Consanguinity↗
PubMed1994

Combined segregation and linkage analysis of Graves disease with a thyroid autoantibody diathesis.

Combined segregation and linkage analysis is a powerful technique for modeling linkage to diseases whose etiology is more complex than the effect of a well-described single genetic locus and for investigating the influence of single genes on various aspects of the disease phenotype. Graves disease is familial and is associated with human leukocyte antigen (HLA) allele DR3. Probands with Graves disease, as well as close relatives, have raised levels of thyroid autoantibodies. This phenotypic information additional to affection status may be considered by the computer program COMDS for combined segregation and linkage analysis, when normals are classified into diathesis classes of increasing thyroid autoantibody titer. The ordinal model considers the cumulative odds of lying in successive classes, and a single additional parameter is introduced for each gene modeled. Distributional assumptions are avoided by providing estimates of the population frequencies of each class. Evidence for linkage was increased by considering the thyroid autoantibody diathesis and by testing two-locus models. The analysis revealed evidence for linkage to HLA-DR when the strong coupling of the linked locus to allele DR3 was considered (lod score of 6.6). Linkage analysis of the residual variation revealed no evidence of linkage to Gm, but a suggestion of linkage to Km.

Adolescent↗
PubMed2005

Genetic and physical mapping of Pi36(t), a novel rice blast resistance gene located on rice chromosome 8.

Blast resistance in the indica cultivar (cv.) Q61 was inherited as a single dominant gene in two F2 populations, F2-1 and F2-2, derived from crosses between the donor cv. and two susceptible japonica cvs. Aichi Asahi and Lijiangxintuanheigu (LTH), respectively. To rapidly determine the chromosomal location of the resistance (R) gene detected in Q61, random amplified polymorphic DNA (RAPD) analysis was performed in the F2-1 population using bulked-segregant analysis (BSA) in combination with recessive-class analysis (RCA). One of the three linked markers identified, BA1126(550), was cloned and sequenced. The R gene locus was roughly mapped on rice chromosome 8 by comparison of the BA1126(550) sequence with rice sequences in the databases (chromosome landing). To confirm this finding, seven known markers, including four sequence-tagged-site (STS) markers and three simple-sequence repeat (SSR) markers flanking BA1126(550) on chromosome 8, were subjected to linkage analysis in the two F2 populations. The locus was mapped to a 5.8 cM interval bounded by RM5647 and RM8018 on the short arm of chromosome 8. This novel R gene is therefore tentatively designated as Pi36(t). For fine mapping of the Pi36(t) locus, five additional markers including one STS marker and four candidate resistance gene (CRG) markers were developed in the target region, based on the genomic sequence of the corresponding region of the reference japonica cv. Nipponbare. The Pi36(t) locus was finally localized to an interval of about 0.6 cM flanked by the markers RM5647 and CRG2, and co-segregated with the markers CRG3 and CRG4. To physically map this locus, the Pi36(t)-linked markers were mapped by electronic hybridization to bacterial artificial chromosome (BAC) or P1 artificial chromosome (PAC) clones of Nipponbare, and a contig map was constructed in silico through Pairwise BLAST analysis. The Pi36(t) locus was physically delimited to an interval of about 17.0 kb, based on the genomic sequence of Nipponbare.

Alleles↗
PubMed1999

Mapping morphological genes relative to molecular markers in lettuce (Lactuca sativa L.)

Two F2 populations were generated by crossing morphologically diverse genetic stocks in order to map 10 morphological traits relative to polymerase chain reaction-based molecular markers (RAPDs). Using one segregating population generated from crossing the experimental line, 'dwarf-2', with the butterhead cultivar, 'Saffier', the dwarf phenotype conditioned by the dwf2 locus was mapped using bulked segregation analysis to within 38 cM of the Adh3 locus. Using the second segregating population generated by crossing two experimental lines, 87-25-1M x 87-109M, nine traits [white seed (w), brown seed (br), salmon flower colour (sa), pale yellow flower colour (pa), virescent juvenile leaf colour (vi), plump involucre (pl), yellow seed (y), one of two complementary genes for anthocyanin expression (C or G) and anthocyanin spotting (Rs)] were linked to RAPD loci, but only six of them could be placed on an existing genetic map of lettuce generated by analysis of cv. 'Calmar' x cv. 'Kordaat'. A tenth trait, golden yellow (gy), remained unlinked. Approximately a third of the RAPD markers analysed segregated in both the 87-25-1M x 87-1090M and 'Calmar' x 'Kordaat' populations. In the genomic regions with multiple segregating loci in common, their relative orders and distances were mostly conserved. In one instance, linkage detected in the present study consolidated two separate groups on the earlier genetic map.

Journal Article↗
PubMed2005

Segregation of chromosomes in sperm of reciprocal translocation carriers: a review.

Reciprocal translocations, the most frequent structural aberration in humans, are mainly transmitted by one of the parents. In order to analyze the chromosomal content of the spermatozoa from carriers of chromosomal reorganizations, two methods have been used, karyotyping of sperm chromosomes by the human-hamster system and fluorescence in situ hybridization (FISH) in decondensed sperm nuclei. In this work, we review 92 sperm chromosome segregation studies from 85 different reciprocal translocation carriers, including a triple translocation carrier. Using the human-hamster method, a total of 5,818 spermatozoa from 44 reciprocal translocation carriers have been analyzed, 43 of them carrying a single reciprocal translocation and one was a carrier of a double reciprocal translocation. A segregation analysis in a carrier of a t(2;22;11) has been also reported. Carrying out FISH in sperm nuclei, a total of 237,042 spermatozoa from 46 reciprocal translocation carriers have been analyzed. Six of these were also analyzed by the human-hamster system. Taking into account both methods, a total of 76 different reciprocal translocations have been studied. In 74 of these 76 translocations, the reorganization occurs between autosomes, and in the other two, the Y chromosome is involved. Although along general lines, there are similarities between the results obtained by the two methods of analysis, variations are observed when the distribution of the different types of segregations that produce imbalances is compared. As a general rule reciprocal translocation carriers produce more unbalanced sperm than normal or balanced sperm. The results reported also corroborate that the proportion of unbalanced forms depends on the characteristics of the reorganization and that it varies widely. Thus the importance of performing a detailed meiotic behavior analysis for each particular translocation in order to obtain enough information to give adequate genetic counseling is stressed. Aspects as to the possible overestimation of 3:1 segregations or the presence of interchromosomal effects still need to be elucidated.

Chromosome Segregation↗
PubMed2000

Combined segregation and linkage analysis of inflammatory bowel disease in the IBD1 region using severity to characterise Crohn's disease and ulcerative colitis. On behalf of the GISC.

Inflammatory bowel disease (IBD) is a chronic relapsing disorder affecting the gastro-intestinal tract and is subdivided into two main subtypes: Crohn's disease (CD) and ulcerative colitis (UC). Although the aetiology of IBD is unknown, a strong genetic susceptibility is suggested and different candidate regions have been identified for both CD and UC. The IBD1 region on chromosome 16 has been confirmed to be important for susceptibility to CD, whereas conflicting evidence has been obtained for UC. We performed a combined linkage and segregation analysis in the identified IBD1 region on a sample of 82 extended families with IBD using a parametric method implemented in the computer program COMDS. This approach allows simultaneous evaluation of linkage while estimating the mode of inheritance and to include severity of the trait to characterise the CD and UC phenotypes. Our results are consistent with the presence of a major gene in the IBD1 region close to D16S408 involved in both UC and CD. Furthermore, our data support evidence that a single mutation in the gene leads more frequently to UC, whereas inheritance of two mutant alleles results in the more severe CD. In our study the IBD1 locus was found to have a major role in IBD predisposition in the Italian population.

Adult↗
PubMed2003

SNP-based codominant markers for a recessive gene conferring resistance to corky root rot (Rhizomonas suberifaciens) in lettuce (Lactuca sativa).

The analysis of F2 progeny and derived F3 families of Lactuca sativa segregating for resistance to corky root rot caused by Rhizomonas suberifaciens permitted the identification of restriction fragment length polymorphism (RFLP) and single nucleotide polymorphism (SNP) markers linked to the recessive resistance gene cor. PCR-based markers were identified by bulked segregant analysis (BSA). Allele-specific primers were generally designed with the 3 terminal base coinciding with an SNP, matching one of the alleles and mismatching the other, and with an additional subterminal 3 base mismatching both alleles. Codominant, robust, and inexpensive molecular markers were obtained that used standardized PCR conditions. Some of the markers could be analyzed in multiple Lactuca mapping populations that did not segregate for disease resistance allowing the cor locus to be located on several maps. The consistent low density of markers around cor in these maps suggests that cor may be in an area with an elevated rate of recombination. Evaluation of these markers in a large sample of cultivars and landraces identified pairs of flanking polymorphic markers that can be used for marker-assisted selection of corky root resistance.

Chromosome Mapping↗
PubMed2003

Using an age-at-onset phenotype with interval censoring to compare methods of segregation and linkage analysis in a candidate region for elevated systolic blood pressure.

BACKGROUND: Genetic studies of complex disorders such as hypertension often utilize families selected for this outcome, usually with information obtained at a single time point. Since age-at-onset for diagnosed hypertension can vary substantially between individuals, a phenotype based on long-term follow up in unselected families can yield valuable insights into this disorder for the general population. METHODS: Genetic analyses were conducted using 2884 individuals from the largest 330 families of the Framingham Heart Study. A longitudinal phenotype was constructed using the age at an examination when systolic blood pressure (SBP) first exceeds 139 mm Hg. An interval for age-at-onset was created, since the exact time of onset was unknown. Time-fixed (sex, study cohort) and time-varying (body mass index, daily cigarette and alcohol consumption) explanatory variables were included. RESULTS: Segregation analysis for a major gene effect demonstrated that the major gene effect parameter was sensitive to the choice for age-at-onset. Linkage analyses for age-at-onset were conducted using 1537 individuals in 52 families. Evidence for putative genes identified on chromosome 17 in a previous linkage study using a quantitative SBP phenotype for these data was not confirmed. CONCLUSIONS: Interval censoring for age-at-onset should not be ignored. Further research is needed to explain the inconsistent segregation results between the different age-at-onset models (regressive threshold and proportional hazards) as well as the inconsistent linkage results between the longitudinal phenotypes (age-at-onset and quantitative).

Adolescent↗
PubMed1997

Markov chain Monte Carlo segregation and linkage analysis for oligogenic models.

A new method for segregation and linkage analysis, with pedigree data, is described. Reversible jump Markov chain Monte Carlo methods are used to implement a sampling scheme in which the Markov chain can jump between parameter subspaces corresponding to models with different numbers of quantitative-trait loci (QTL's). Joint estimation of QTL number, position, and effects is possible, avoiding the problems that can arise from misspecification of the number of QTL's in a linkage analysis. The method is illustrated by use of a data set simulated for the 9th Genetic Analysis Workshop; this data set had several oligogenic traits, generated by use of a 1,497-member pedigree. The mixing characteristics of the method appear to be good, and the method correctly recovers the simulated model from the test data set. The approach appears to have great potential both for robust linkage analysis and for the answering of more general questions regarding the genetic control of complex traits.

Computer Simulation↗
PubMed2006

Autosomal dominant mutation causing the dorsal ridge predisposes for dermoid sinus in Rhodesian ridgeback dogs.

OBJECTIVES: To define the mode of inheritance of the dorsal ridge and investigate if the ridge predisposes to the congenital abnormality dermoid sinus in the Rhodesian ridgeback. METHODS: Segregation analysis was performed, including 87 litters (n=803) produced in Sweden between 1981 and 2002. Data were corrected to avoid bias in the segregation ratio. Chi-squared analysis was performed including 402 litters (n=3598) for the evaluation of a possible genetic correlation between the ridge and dermoid sinus. RESULTS: The ridge is inherited in an autosomal dominant mode and predisposes for dermoid sinus. The frequency of ridgeless offspring in the Swedish Rhodesian ridgeback population is estimated to be 5.6 per cent. CLINICAL SIGNIFICANCE: Rhodesian ridgeback dogs that carry the ridge trait are predisposed to dermoid sinus.

Animals↗
PubMed1989

Genetic polymorphism for human platelet thermostable phenol sulfotransferase (TS PST) activity.

Platelet TS PST basal activity and thermal stability were measured in blood samples from 237 individuals in 50 nuclear families. Significant correlations were found among first degree relatives, confirming the previously reported familial aggregation of TS PST basal activity and thermal stability. Commingling analysis of basal TS PST activity provided evidence for multiple component distributions, and after transformation to remove skewness, segregation analysis supported a major gene hypothesis. For TS PST thermal stability, commingling analysis also provided evidence for multiple component distributions. However, segregation analyses were equivocal with regard to the presence of a major gene for thermal stability, since support for a major gene model depended on skewness. Bivariate commingling analysis, which examined thermal stability by simultaneously considering basal activity and activity after heating, suggested that genotypes, as defined by the inferred component distributions for TS PST activity, differ in thermal stability. A three-allele model is proposed as one hypothesis that may account for the combined results of basal activity and thermal stability. The results of this study indicate that a major gene polymorphism in conjunction with polygenic inheritance plays an important role in the regulation of both level of activity and thermal stability of this important drug-metabolizing enzyme in humans.

Adolescent↗
PubMed1996

Pedigree analysis package vs. MIXD: fitting the mixed model on a large pedigree.

Results of a simulation study with two methods of analysis of data simulated under the mixed model on a 232-member pedigree are presented. The programs Pedigree Analysis Package (PAP), which approximate the likelihoods needed in a complex segregation analysis, and MIXD, which uses Monte Carlo Markov chain (MCMC), to estimate likelihoods were used. PAP obtained unbiased estimates of the major locus genotype means and the gene frequency, but biased estimates of the environmental variance component, and thus the heritability. A substantial fraction of the runs did not converge to an internal set of parameter estimates when analyzed with PAP. MIXD, which uses the Gibbs sampler to perform the MCMC sampling, produced unbiased estimates of all parameters with considerably more accuracy than obtained with PAP, and did not suffer from convergence of estimates to the boundary of the parameter space. The difference in behavior and accuracy of parameter estimates between PAP and MIXD was most apparent for models with either high or low residual additive genetic variance. Thus in situations where accuracy of the model is important, use of MCMC methods may be useful. In situations where less accuracy is needed, approximation methods may be adequate. Practical issues in using MCMC as implemented in MIXD to fit the mixed model are also discussed. Results of the simulations indicate that, unlike PAP, the starting configurations of most parameter estimates do not substantially influence the final parameter estimates in analysis with MIXD.

Analysis of Variance↗
PubMed2000

Quantitative genetic analysis of circulating levels of biochemical markers of bone formation.

Carboxyterminal propeptide of type 1 collagen (PICP) and bone Gla-protein-osteocalcin (BGP) are the most important components of the organic bone matrix and play a key role in bone formation. To investigate whether and to what extent variation of the plasma levels of these indices of bone turnover depends on genetic factors, we studied 355 adults belonging to nuclear pedigrees. Genetic analysis was carried out in 2 steps: 1) variance decomposition analysis was performed using the FISHER statistical package; and 2) complex segregation analysis implemented in the program package MAN. The effect of age and gender differences, gender hormones, as well as PTH and vitamin-D (calcidiol) plasma levels were evaluated simultaneously with the parameters of variance analysis. The results showed that about 50% of PICP variation is attributable to genetic factors. The effect of age was significant among men and postmenopausal women, whereas calcidiol influenced variation of PICP in premenopausal women. The results of variance analysis showed that some 40% of BGP, adjusted for confounding variables, can be explained in genetic factors. Age and PTH were important covariates for osteocalcin in men and premenopausal women. Exploration of the maximum likelihood estimates of the various hypotheses concerning the mode of intergenerational transmission of PICP and BGP demonstrated a good correspondence to the Mendelian mode of inheritance (i.e., major gene effect).

Adolescent↗